Infected wounds can result in complex clinical complications and delayed healing, presenting a significant global public health challenge. This study explored the effects of topical application of two probiotics, Lactobacillus rhamnosus GG (LGG) and Bifidobacterium animalis subsp. lactis BB-12, on the microenvironment of infected wounds and their impact on wound healing. LGG and BB-12 were applied separately and topically on the Staphylococcus aureus (S. aureus)-infected skin wounds of the rat model on a daily basis. Both probiotics significantly accelerated wound healing, demonstrated by enhanced granulation tissue formation and increased collagen deposition, with BB-12 showing superior efficacy. LGG and BB-12 both effectively inhibited neutrophil infiltration and decreased the expression of pro-inflammatory cytokines tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6). Notably, BB-12 markedly reduced IL-6 levels, while LGG significantly lowered TNF-α, transforming growth factor-β (TGF-β) and vascular endothelial growth factor (VEGF). Additionally, both probiotics promoted macrophage polarization towards the anti-inflammatory M2 phenotype. Microbiota analysis revealed that LGG and BB-12 significantly decreased the abundance of pathogenic bacteria (e.g. Staphylococcus and Proteus) and increased the proportion of beneficial bacteria (e.g. Corynebacterium). Particularly, BB-12 was more effective in reducing Staphylococcus abundance, whereas LGG excelled in promoting Corynebacterium growth. These findings suggest the ability of LGG and BB-12 to modulate the wound microenvironment, enhance wound healing and provide valuable insights for the management of infected wounds.© 2024 The Author(s). Microbial Biotechnology published by John Wiley & Sons Ltd.